Question

Briefly describe two mechanisms that contribute to preserving genome stability (DNA replication accuracy).

Answer 1

The cell has multiple mechanisms to ensure the accuracy of DNA replication.

The first mechanism is the use of a faithful polymerase enzyme that can accurately copy long stretches of DNA. The second mechanism would be for the polymerase to catch its own mistakes and correct them.

Stem cells have an extra safeguard to preserve the accuracy of their genetic information. DNA is double-stranded. The strands split apart and serve as templates for new copies. Every time a stem cell replicates its DNA and splits into two cells, the cell that remains a stem cell will keep the same strand of DNA. This strand is called the mother strand or the immortal strand. In this way, the stem cell can preserve the original copy of its DNA.

Replication

Replication is semi-conservative: newly replicated helices contain an original strand and a newly synthesized one. The original strand serves as a template for the creation of the new strand. Helicase enzymes unzip the double helix structure to expose the two template strands. The enzyme DNA polymerase is responsible for reading each nucleotide on a template strand and adding the complementary base on the elongating new strand. For example, when the polymerase encounters a G base on a template strand, it adds to the new strand a sugar-phosphate unit containing a C base.

Fidelity and Processivity

Not all polymerases are equal. A bacterial cell can have multiple different polymerases. For DNA replication in bacteria called E. coli, DNA polymerase III is the one for the job. DNA Polymerase III has high fidelity -- meaning it’s accurate -- and high processivity -- meaning it can hold on to the DNA for a long time before falling off. For comparison, DNA Polymerase I can only make a DNA chain 20 building blocks long before falling off, while DNA Polymerase III can make a chain that is thousands of units long

Proofreading

DNA polymerase is a remarkable enzyme. Not only does it assemble new DNA strands one base at a time, it also proofreads the new strand as it proceeds. The enzyme can detect an incorrect base on the new strand, back up one sugar unit, snip out the bad base, replace it with the correct base and resume replicating the template strand. The ability to snip out the incorrect base, called exonuclease activity, is built into the DNA polymerase complexes. Proofreading results in an accuracy rate of about 99 percent.

The Immortal Strand

When a cell divides, it replicates its DNA by splitting apart double-stranded DNA and makes new copies along the single strands of the original DNA. The original DNA, which is now part of a double-strand containing new DNA, randomly splits between the two dividing cells. Some types of adult stem cells, however, have non-random segregation of the original DNA strand. By always keeping the original DNA strands, it ensures that it maintains the original information. The original DNA strands are referred to as the immortal strands.

Mismatch Repair

Accurate replication is important enough that cells have evolved a secondary error correction mechanism called DNA mismatch repair to fix the mistakes that DNA polymerase misses. The repair machinery detects mismatches by inspecting the DNA helix structure for deformities. The Mut family of enzymes detects a mismatch, identifies the newly copied strand, finds a suitable location to cleave the strand and removes the portion containing the mismatch. DNA polymerase then resynthesizes the removed portion. Unlike with the single-base repair that DNA polymerase performs while proofreading, the mismatch repair mechanism may replace thousands of bases to make one repair.

Constant Surveillance

The cell ensures the integrity of its DNA even before replication starts. The cell is constantly monitoring the status of its DNA. The moment DNA damage occurs, there are proteins that detect this damage and tell the cell to stop everything so there is time to repair the damage. Chromatin, which is the combination of DNA packaged neatly by proteins, also detects DNA damage and changes shape to recruit DNA repair proteins to the site of damage.